Variant report

Variant	rs11737560
Chromosome Location	chr4:120131644-120131645
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:120125197..120131905-chr4:120131994..120135569,17	K562	blood:
2	chr4:120059391..120062207-chr4:120131058..120133617,2	MCF-7	breast:
3	chr4:120125730..120127541-chr4:120130330..120131994,2	MCF-7	breast:
4	chr4:120013479..120014990-chr4:120129629..120131701,2	MCF-7	breast:
5	chr4:120130951..120136158-chr4:120218006..120223072,8	K562	blood:
6	chr4:119903589..119905538-chr4:120130770..120132703,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178636	Chromatin interaction
ENSG00000145390	Chromatin interaction
ENSG00000164096	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11725433	0.90[ASN][1000 genomes]
rs11729857	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11733606	0.90[ASN][1000 genomes]
rs11734808	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs13104050	0.90[ASN][1000 genomes]
rs13106878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13113462	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs13113662	0.90[ASN][1000 genomes]
rs13127517	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs13140255	0.90[ASN][1000 genomes]
rs13144426	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs1397611	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs1511021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1511022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17050312	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs17334151	0.90[ASN][1000 genomes]
rs17517075	0.85[ASN][1000 genomes]
rs34156358	0.90[ASN][1000 genomes]
rs34478210	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34624042	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34951506	0.90[ASN][1000 genomes]
rs35137697	0.90[ASN][1000 genomes]
rs35612705	0.90[ASN][1000 genomes]
rs35646004	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs35830965	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62326356	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62328380	0.90[ASN][1000 genomes]
rs62328402	0.90[ASN][1000 genomes]
rs62328403	0.90[ASN][1000 genomes]
rs62328404	0.90[ASN][1000 genomes]
rs6846936	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71610255	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7655064	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7678138	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv948802	chr4:119844269-120208926	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv1008115	chr4:120007913-120143849	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
4	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11737560	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs11737560	RP11-33B1.1	cis	Thyroid	GTEx
rs11737560	USP53	cis	Whole Blood	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120101000-120132400	Weak transcription	Left Ventricle	heart
2	chr4:120117600-120133200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:120125800-120131800	Enhancers	HSMM	muscle
4	chr4:120125800-120132200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr4:120126200-120132200	Enhancers	NHDF-Ad	bronchial
6	chr4:120126400-120132200	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr4:120126400-120132400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr4:120126400-120132400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr4:120126400-120132400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr4:120126400-120132400	Enhancers	HUVEC	blood vessel
11	chr4:120126400-120132600	Weak transcription	Right Atrium	heart
12	chr4:120127400-120132200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr4:120127400-120132400	Enhancers	NHLF	lung
14	chr4:120128000-120132800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr4:120128400-120132400	Weak transcription	Adipose Nuclei	Adipose
16	chr4:120128600-120132400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr4:120128600-120132400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr4:120128600-120132600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr4:120129000-120132800	Weak transcription	Fetal Heart	heart
20	chr4:120129200-120132400	Weak transcription	Fetal Lung	lung
21	chr4:120129400-120132200	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr4:120129600-120131800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr4:120129600-120132200	Enhancers	Muscle Satellite Cultured Cells	--
24	chr4:120129600-120132200	Enhancers	HMEC	breast
25	chr4:120129600-120132800	Enhancers	Hela-S3	cervix
26	chr4:120129800-120132400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr4:120130000-120132600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr4:120130400-120132400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr4:120130600-120132800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:120130800-120131800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr4:120130800-120132600	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr4:120130800-120132800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr4:120131000-120132000	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr4:120131000-120132400	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr4:120131000-120132800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr4:120131200-120131800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr4:120131200-120131800	Enhancers	NHEK	skin
38	chr4:120131200-120132000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr4:120131200-120132200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr4:120131200-120132200	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr4:120131200-120132200	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr4:120131200-120132200	Weak transcription	A549	lung
43	chr4:120131200-120132200	Weak transcription	K562	blood
44	chr4:120131200-120132400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr4:120131200-120132400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr4:120131200-120132400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr4:120131200-120132400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr4:120131200-120132400	Weak transcription	NH-A	brain
49	chr4:120131200-120132800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr4:120131200-120132800	Weak transcription	Stomach Mucosa	stomach

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